Abstract: Methods for isolating and using multi-protein complexes that are biologically active are provided. The complexes contain one or more proteins of interest (e.g. a receptor, ion channel, etc.) and associates scaffolding proteins such as phosphatases, kinases and post synaptic density components. Buffers that do not contain denaturing agents and which may be used to isolate the multi-protein complexes are also provided, as are protein arrays containing the biologically active multi-protein complexes. The protein arrays may be used, for example, for high throughput screening assays.

Abstract: Novel peptides are described which comprise an amino acid motif selected from the group consisting of “PG”, “GP”, “PI” and “IG” and having up to 10 amino acids upstream and/or downstream of the amino acid motif, wherein “P” in the motif is proline or hydroxyproline and the peptide stimulates the development, maintenance and repair of bone, cartilage and associated connective tissue. The invention further relates to pharmaceutical compositions of these peptides, as well as therapeutic and prophylactic uses of such peptides.

Abstract: This invention relates to bioluminescent methods for detecting specific target bacteria, such as E. coli, coliforms, Enterococcus spp, Listeria spp and S. aureus in samples. The sample to be tested is incubated in a non-selective growth medium for up to 8 hours to produce a sample culture and which is then mixed with detection reagents. The detection reagents include a lysis reagent which disrupts bacterial cells in the sample, a pro-luciferin molecule which is specifically converted into luciferin by said target bacteria; and luminescence reagents which produce a luminescent signal in the presence of luciferin. The mixture of sample culture and detection reagents is then incubated and the luminescent signal from the reaction mixture measured.

Abstract: The invention concerns a medium for detecting, identifying and differentiating a microorganism strain in a liquid medium by contacting said liquid sample with a combination of chromogens substrates of enzymes expressed or not by the strain to be detected, the final coloration of the mixture being detectable in the wavelengths of the visible light.

Abstract: The disclosure provides compositions and methods to determine or detect ADP or the activity of enzymes, including phosphotransferases such as kinases (e.g., protein, lipid, and sugar kinases) and ATP hydrolases such as ATPases, e.g., HSP90, that employ ATP as a substrate and form ADP as a product by monitoring changes in ADP.

Abstract: Methods of treating and evaluating subjects having neoactive mutants are described herein.

Abstract: Provided is a preventive, progression inhibitor or remedy for a disease one of the causes of which is the activation of the P13K/AKT signaling pathway or vice versa. A phosphorylation-inhibiting and/or dephosphorylating agent, which has an effect of inhibiting the phosphorylation at least at one of the phosphorylation sites of PTEN protein selected from the group consisting of T382, T383 and S380 and/or an effect of dephosphorylating the same, is prepared. Alternatively, a phosphorylation-inhibiting or dephosphorylating agent for PTEN is screened by a method comprising a step for confirming an ability of a test substance to inhibit the phosphorylation at least at one of the phosphorylation sites of PTEN protein selected from the group consisting of T382, T383 and S380 or a dephosphorylation ability thereof. Then, a substance having an effect opposite to the inhibition of PTEN phosphorylation or dephosphorylation thereof, e.g.

Abstract: Tyrosine phosphorylation, regulated by protein tyrosine phosphatases (PTPs) and kinases (PTKs), is important in signaling pathways underlying tumorigenesis. A mutational analysis of the tyrosine phosphatase gene superfamily in human cancers identified 83 somatic mutations in six PTPs (PTPRF, PTPRG, PTPRT, PTPN3, PTPN13, PTPN14), affecting 26% of colorectal cancers and a smaller fraction of lung, breast and gastric cancers. Fifteen mutations were nonsense, frameshift or splice site alterations predicted to result in truncated proteins lacking phosphatase activity. Five missense mutations in the most commonly altered PTP (PTPRT) were biochemically examined and found to reduce phosphatase activity. Expression of wild-type but not a mutant PTPRT in human cancer cells inhibited cell growth. These observations suggest that the tyrosine phosphatase genes are tumor suppressor genes, regulating cellular pathways that may be amenable to therapeutic intervention.

Abstract: Methods of assaying for disease-associated crystal species in biological samples are described. Such methods involve contacting a patient sample with an excess of a detectable crystal-tagging compound reactive with a plurality of crystal species under conditions that allow the detectable crystal-tagging compound to react with a plurality of crystal species, if present, to form tagged crystal species complexes. Substantially all unreacted tagging compound is then removed. If desired, chemical, enzymatic, or physical treatment can be used to selectively degrade some, but not, of the tagged crystal species. Assessment of soluble versus crystal-associated label is then performed.

Abstract: Compositions, methods, and kits for detecting and monitoring kinase, phosphatase and protein post-translational modification activity are described. The compositions typically include a peptide, a detectable moiety, and a protease cleavage site. Modification of a peptide by a kinase, phosphatase or other protein post-translational modification alters the proteolytic sensitivity of the peptide, resulting in a change of a detectable property of the composition. Panel assays for determining substrates or modulators of kinase, phosphatase or other protein post-translational modification activity are also described.

Abstract: Disclosed is a method for diagnosing melanoma in a human subject, as well as a method for providing a prognosis to a human subject who is at risk of developing melanoma recurrence, and a method for determining the stage of melanoma in a human subject, comprising the step of determining the level of expression of phosphatase and actin regulator 1 (PHACTR1) gene, or fragments thereof, either alone or in combination with the level of expression of secreted integrin-binding phosphoprotein (SPP1), preferentially expressed antigen in melanoma (PRAME), growth differentiation factor 15 (GDF 15), and chemokine C-X-C motif ligand 10 (CXCL10) genes. Further, the invention relates to a diagnostic kit, comprising at least one substance for detection of the expression of PHACTR1, or fragments thereof, either alone or in combination with the detection of SPP1, PRAME, GDF15, and CXCL10, for the diagnosis or prognosis of melanoma.

Abstract: The invention relates to a method of diagnosing or monitoring multiple sclerosis.

Abstract: The present invention relates to a forensic test strip and method for the detection of semen. This strip is comprised of a paper element coated with reagents which react to the presence of acid phosphatase (AP), an enzyme found in semen, and is sandwiched between a clear plastic cover and an opaque plastic backing. This assembly is peeled apart, the paper element exposed to a source of semen, and the clear cover replaced. A positive test is characterized by a bright purple color, which easily can be seen through the clear cover. An adhesive backing is provided, which allows an investigator conveniently to affix the test strip directly to a notebook.

Abstract: Methods and compositions relating to CDP-taxane conjugates are described herein.

Abstract: The present invention relates to methods of detecting, in a sample, embryonic stem cells, induced pluripotent stem cells, and/or cells undergoing reprogramming to produce induced pluripotent stem cells. These methods include providing a sample potentially containing such cells and providing a rosamine derivative compound of the formula (I): where the rosamine derivative compound selectively produces fluorescent signals for embryonic stem cells, induced pluripotent stem cells, and/or cells undergoing reprogramming to produce induced pluripotent stem cells. These methods also include the steps of contacting the sample with the rosamine derivative compound and detecting the presence of the embryonic stem cells, induced pluripotent stem cells, and/or cells undergoing reprogramming to produce induced pluripotent stem cells based on fluorescent signals emitted by the sample following said contacting.

Abstract: The subject invention relates in part to the surprising and unexpected discovery that insects that are resistant to Bacillus thuringiensis Cry toxins have measurably altered alkaline phosphatase (ALP) activity as compared to insects that are susceptible to Cry toxins. This and other surprising discoveries reported herein have broad implications in areas such as managing and monitoring the development of insect resistance to B. t. toxins. For example, the subject invention provides a simple and fast assay (enzymatic or otherwise) for detecting ALP activity levels and thereby monitoring the development of resistance by insects to crystal protein insect toxins. There was no prior motivation or suggestion to go about resistance monitoring using this simple and easy approach.

Abstract: Methods and kits for performing a two-phase optical assay for one or more than one analyte without intrinsic optical contrast in a sample are disclosed. The method requires use of a functionalized microparticle immobilized with two or more than functional components and an additional set of one or more than one functional component. The assay can be performed in one single container and does not need a wash step.

Abstract: The present invention relates to transgenic animals, as well as compositions and methods relating to the characterization of gene function. Specifically, the present invention provides transgenic mice comprising disruptions in PRO69122, PRO204, PRO214, PRO222, PRO234, PRO265, PRO309, PRO332, PRO342, PRO356, PRO540, PRO618, PRO944, PRO994, PRO1079, PRO1110, PRO1122, PRO1138, PRO1190, PRO1272, PRO1286, PRO1295, PRO1309, PRO1316, PRO1383, PRO1384, PRO1431, PRO1434, PRO1475, PRO1481, PRO1568, PRO1573, PRO1599, PRO1604, PRO1605, PRO1693, PRO1753, PRO1755, PRO1777, PRO1788, PRO1864, PRO1925, PRO1926, PRO3566, PRO4330, PRO4423, PRO36935, PRO4977, PRO4979, PRO4980, PRO4981, PRO5801, PRO5995, PRO6001, PRO6095, PRO6182, PRO7170, PRO7171, PRO7436, PRO9912, PRO9917, PRO37337, PRO37496, PRO19646, PRO21718, PRO19820, PRO21201, PRO20026, PRO20110, PRO23203 or PRO35250 genes.

Abstract: This invention relates to the finding that collagen peptides bind to the osteoclast-associated receptor (OSCAR) and stimulate the activation and/or differentiation of OSCAR expressing cells, such as osteoclasts and osteoclast precursor cells. Collagen peptides are described which may be useful in the modulation of the differentiation and/or activation of OSCAR expressing cells, for example in the treatment of bone defects and disorders characterized by altered differentiation and/or activation of OS-CAR expressing cells.

Abstract: The present invention provides a method for the detection of testicular cancer and/or precursors hereof by screening a sample for the presence of at least two markers in the same cell, wherein the sample is a semen sample and/or an ejaculate from a male human being.

Abstract: The present invention provides for methods and systems for detecting steroids. Examples of such steroids include estrogen, progesterone, androgen, testosterone, and derivatives and analogs thereof. Systems useful for carrying out the method include tripartite constructs including a DNA-binding domain, a ligand binding domain, and an activation domain. The present invention provides numerous improvements over previous diagnostic systems for detection of steroids, such advantages include that the method allows for detection of steroid analogs and derivatives, whose structures may not yet be known, the method is generally applicable to a wide variety of organisms, and numerous ligand binding domains may be used in conjunction with the present system.

Abstract: The present invention is directed to a method for determining if a subject is at increased risk to develop obesity or pathology related to obesity by determining the presence of a haplotype comprising three specific SNPs in a DNA or RNA sample of this subject and/or an elevated serum ENPP1 protein concentration. The present invention also relates to a kit and to an isolated nucleic sequence, vector or recombinant cell comprises said ENPP1 gene haplotype. The invention further comprises a method for selecting a compound for the treatment or the prevention of obesity or pathology related to obesity and a method for determining the efficacy of a drug to reduce the risk of obesity or pathology related to obesity in a patient.

Abstract: The invention relates to diagnostic and prognostic assays and kits for pulmonary hypertension (PH) and types thereof. The invention includes detecting the expression level of markers associated with pulmonary hypertension for diagnosis, prognosis, or treatment of pulmonary hypertension.

Abstract: A cut-point in the quantitative measurement of PTEN protein expression that accurately identifies tumors with two inactivated alleles of the PTEN gene. Patients with a normalized PTEN score of PTEN null will be treated with a pan-ErbB tyrosine kinase inhibitor. A normalized PTEN protein expression score is obtained by comparing the tumor PTEN OD expression value with the non-malignant PTEN OD expression value.

Abstract: Kits for the assay of enzymes involved in post-translational modifications are provided. The kits facilitate the execution of methods of assay that allow for convenient and accurate analysis using atomic mass spectrometry of post-translation modifications of substrates by enzymes involved in post-translational modifications, including kinase and phosphatase enzymes.

Abstract: Methods and devices are provided for the rapid and specific detection of target microorganisms, cells, and the like. In one embodiment, the methods involve contacting a target microorganism (e.g., in a sample) with a permeabilization reagent that selectively permeabilizes or lyses the microorganism; contacting the selectively permeabilized microorganism with a detection reagent that is taken into the selectively permeabilized organism or that contacts metabolites or enzymes released by the selectively permeabilized microorganism, where the detection reagent produces a signal in the presence of said metabolites or enzymes; and detecting a signal produced by the detection reagent in the presence of the metabolites or enzymes wherein the strength of the signal indicates the presence and/or amount of the target microorganism in the sample.

Abstract: The present invention involves the identification and preparation of vascular endothelial growth factor-E (VEGF-E). VEGF-E is a novel polypeptide related to vascular endothelial growth factor (VEGF) and bone morphogenetic protein 1. VEGF-E has homology to VEGF including conservation of the amino acids required for activity of VEGF. VEGF-E can be useful in wound repair, as well as in the generation and regeneration of tissue.

Abstract: A method for producing a plant with increased yield as compared to a corresponding wild type plant whereby the method comprises at least the following step: increasing or generating in a plant or a part thereof one or more activities selected from the group consisting of 17.6 kDa class I heat shock protein, 26.

Abstract: The present invention provides a novel mechanistic pathway and methods related to this pathway for the identification of compounds for the treatment of diseases involving cell proliferation, invasion and/or metastasis such as cancer. In particular, the instant invention relates to the phosphatase activity of Eya and the Eya-Six complex as a target for identifying novel therapeutic agents for the treatment of proliferative, invasive and/or metastatic disorders, and compositions identified using the methods disclosed herein.

Abstract: This document relates to the activity of interferon regulatory factor 4 (IRF4) in T-cell lymphomas. For example, methods and materials involved in reducing the expression of an IRF4 polypeptide in T-cell lymphoma cells and identifying agents having the ability to reduce expression of an IRF4 polypeptide in T-cell lymphoma cells are provided. This document also relates to reducing DUSP22 or FLJ43663 polypeptide activity in T-cell lymphomas. For example, methods and materials involved in reducing the expression of DUSP22 polypeptides and/or FLJ43663 polypeptides in T-cell lymphoma cells and identifying agents having the ability to reduce expression of DUSP22 polypeptides and/or FLJ43663 polypeptides in T-cell lymphoma cells are provided.

Abstract: Human pluripotential embryonic stem cell cultures are provided, as are human feeder cells useful for growing the human embryonic stem cells, conditioned medium obtained from cultures of the human feeder cells, and factors derived from the conditioned medium. Also provided are methods of growing human embryonic stem cells in the presence of the human feeder cells, the conditioned medium, the factors derived from the conditioned medium, or a combination thereof. In addition to the human embryonic stem cell cultures grown according to such methods, isolated human embryonic stem cells obtained from such human embryonic stem cell cultures are provided, as are methods of using such isolated cells.

Abstract: The present technology relates to methods and systems for detection of pyrophosphate. As such, disclosed herein are methods and systems that permit improved pyrophosphate detection. Also disclosed herein are methods and systems which utilize improved pyrophosphate detection for nucleotide sequencing.

Abstract: The invention relates to the treatment and diagnosis of organ dysfunction caused by ischemia reperfusion injury. In particular, the invention relates to sphinganine-1-phosphate, a sphingolipid metabolite, and its use in the diagnosing, preventing, and/or treating ischemia reperfusion-associated disorders, including, without limitation, disorders of the kidney, liver, lung, brain, and heart.

Abstract: Compositions, methods, and kits for detecting and monitoring kinase, phosphatase and protein post-translational modification activity are described. The compositions typically include a peptide, a detectable moiety, and a protease cleavage site. Modification of a peptide by a kinase, phosphatase or other protein post-translational modification alters the proteolytic sensitivity of the peptide, resulting in a change of a detectable property of the composition. Panel assays for determining substrates or modulators of kinase, phosphatase or other protein post-translational modification activity are also described.

Abstract: Division arrested cells are used in screening assays to determine the effect of a substance of interest on the cells. The division arrested cells can be used in drug screening assays, signal transduction assays, and are especially useful in large scale, high throughput assays.

Abstract: Provided herein are methods for the diagnosis, staging, prognosis, or management of liver disease, e.g. chronic liver disease, and other diseases using profiles of the ubiquitin-proteasome system determined from acellular body fluids or cell-containing samples. Further provided are methods of predicting response to therapy in certain populations of patients with liver disease.

Abstract: The present invention provides methods of detecting cancer using biomarkers.

Abstract: A method of selecting a population of adherent cells of a placenta tissue suitable for transplantation is disclosed. The method comprising: (a) determining prior to transplantation in a candidate population of adherent cells of a placenta tissue at least one of the following parameters: (i) percentage of viable cells in the candidate population; (ii) immune phenotype of cells in the candidate population; (iii) xeno-contamination in the candidate population; (iv) sterility of the candidate population; and (v) immunosuppressive activity of cells in the candidate population; and (b) selecting or excluding the candidate population according to predetermined values of at least one of the parameters, thereby selecting a population of adherent cells of the placenta tissue suitable for transplantation.

Abstract: The present invention provides methods that are useful for the diagnosis of neurodegenerative disease or disorder and for the screening of compounds or therapeutic agents for treating a neurodegenerative disease or disorder. The methods pertain in part to the correlation of a neurodegenerative disease or disorder with abnormal or altered endoplasmic reticulum-mitochondrial-associated membranes (ER-MAM) integrity.

Abstract: The subject invention relates in part to the surprising and unexpected discovery that insects that are resistant to Bacillus thuringiensis Cry toxins have measurably altered alkaline phosphatase (ALP) activity as compared to insects that are susceptible to Cry toxins. This and other surprising discoveries reported herein have broad implications in areas such as managing and monitoring the development of insect resistance to B.t. toxins. For example, the subject invention provides a simple and fast assay (enzymatic or otherwise) for detecting ALP activity levels and thereby monitoring the development of resistance by insects to crystal protein insect toxins. There was no prior motivation or suggestion to go about resistance monitoring using this simple and easy approach.

Abstract: The invention relates to methods and kits for detecting thyroid cancer by detecting differences in the expression of genes that are differentially expressed in thyroid cancer cells.

Abstract: The invention provides tools for management of patients diagnosed with ankylosing spondylitis and prior to the initiation of therapy with an anti-TNFalpha agent. The tools are specific markers and algorithms of predicting response to therapy based on standard clinical primary and secondary end-points using serum marker concentrations. In one embodiment the baseline level of leptin or osteocalcin is used to predict the response at Week 14 after the initiation of therapy. In another embodiment, the change in a serum protein biomarker after 4 weeks of therapy is used such as complement component 3.

Abstract: Aspects of the invention relate to a method for inhibiting the growth of a microbe that expresses bacterial vitamin K epoxide reductase (bVKOR). The method involves contacting the bacterial cell with an effective amount of an agent that inhibits bVKOR. Agents include a drug, ligand or portion thereof, protein, polypeptide, small organic molecule, antisense nucleic acid, RNAi, or antibody. Examples of useful agents are a phenylpropanoid, a modified phenylpropanoid, a coumarin or modified coumarin. A particularly useful agents is warfarin or a variant thereof or ferulenol or a variant thereof. The microbe is any microbe carrying a bVKOR gene, such as Mycobacterium tuberculosis.

Abstract: Methods and compositions relating to CDP-taxane conjugates are described herein.

Abstract: Methods of inhibiting S. aureus propagation, and screening for compounds that inhibit S. aureus propagation, are described. A method of inhibiting S. aureus propagation comprises inhibiting ribosomal binding of a specific S. aureus tRNA in the S. aureus by an amount sufficient to inhibit S. aureus protein expression. A method of screening for compounds useful for inhibiting S. aureus propagation comprises contacting a specific S. aureus tRNA to a ribosome that binds that tRNA in the presence of the test compound, and then determining whether the compound inhibits the binding of that tRNA.

Abstract: A method for diagnosing an early stage melanoma which includes detecting the expression level of dual specificity phosphatase 1 protein (DUSP1) and a method for determining a prognosis for a subject having melanoma which includes detecting the expression level of DUSP1 are disclosed. Also disclosed are pharmaceutical compositions and kits comprised by these methods.

Abstract: The present invention is directed to a composition comprising a vanadium-containing phosphatase inhibitor and a polyol. In the presence of the polyol the effect of the inhibitor is enhanced, even in the presence of chelating agents or reducing agents. The invention also concerns the use of the inventive composition for inhibiting a phosphatase, as well as kits comprising the composition.

Abstract: The invention relates to a method for characterizing, in particular for quantifying molecular marker(s) that are intracellularly absorbed from tissues by blood macrophages that are recirculated from the tissues into the circulatory system, wherein the following steps are carried out: application of an agent to whole blood, said agent inhibiting coagulation and/or agglomeration of whole blood; selecting and/or enriching and/or separating blood macrophages or leukocyte populations that contain blood macrophages from whole blood; perforating and/or lysing the selected blood macrophages or leukocyte populations containing the blood macrophages, optionally after previous permeabilization thereof; qualitatively and quantitatively determining non blood macrophage markers, namely molecular markers arising from tissue, after previously perforating and/or lysing the blood macrophages or leukocyte populations containing the blood macrophages, and an apparatus for carrying out the method.

Abstract: This invention is directed towards methods of destabilizing proteins in living cells, and their use for the development of novel assays. In one embodiment, the invention comprises the use of non-cleavable multimerized ubiquitin fusion proteins to destabilize a target protein, such as a reporter moiety. In one aspect of this method the constructs also comprises a linker that operatively couples the reporter moiety to the multimerized ubiquitin fusion protein. In this embodiment, enzymatic modification of the linker results in a modulation of the coupling of the reporter protein to the multimerized ubiquitin domains resulting in a change in the stability of the reporter moiety. The level of the reporter moiety in the cell can then be used as a measure of the enzymatic activity in the cell. In another embodiment the invention provides for a generalized way of coordinately regulating the cellular concentration of a plurality of target proteins.

Abstract: A method of diagnosing or monitoring a psychotic disorder, or predisposition thereto, comprises measuring, in a sample taken from a subject, the levels of one or more peptide biomarkers listed herein.